Most Japanese also use something called Line. It's both a phone and computer application (by a company called Naver). It's a combo of Skype and Facebook in that it has a timeline function, instant messaging (like whatsapp), stickers, but also has free voice call. It's very useful because most Japanese people check it even more often than they would Skype. Most of my friends in Japan don't even have skype, they only have Line.

Skype is the best way to communicate with people across the globe.